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Manganese in PDB 7xis: Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester

Enzymatic activity of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester

All present enzymatic activity of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester:
3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester, PDB code: 7xis was solved by H.Lu, Y.Komukai, K.Usami, Y.Guo, X.Qiao, M.Nukaga, T.Hoshino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.93 / 1.88
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.121, 62.121, 83.742, 90, 90, 90
R / Rfree (%) 21.3 / 24.1

Other elements in 7xis:

The structure of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester (pdb code 7xis). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester, PDB code: 7xis:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7xis

Go back to Manganese Binding Sites List in 7xis
Manganese binding site 1 out of 2 in the Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:22.3
occ:1.00
 OAJ A:E58203 1.9 40.1 1.0
OE2 A:GLU58 1.9 23.3 1.0
OD1 A:ASP78 2.0 24.6 1.0
OD1 A:ASP23 2.0 27.0 1.0
CG A:ASP78 2.8 28.1 1.0
CD A:GLU58 2.8 25.2 1.0
OAA A:E58203 2.8 75.2 1.0
CAI A:E58203 2.9 58.0 1.0
OD2 A:ASP78 2.9 25.9 1.0
OE1 A:GLU58 3.0 22.6 1.0
CG A:ASP23 3.0 26.4 1.0
MN A:MN202 3.2 32.9 1.0
CAE A:E58203 3.2 69.8 1.0
OD2 A:ASP23 3.4 28.9 1.0
O A:HOH310 3.4 22.7 1.0
O A:GLY24 3.8 28.9 1.0
CAB A:E58203 4.0 74.8 1.0
OAH A:E58203 4.1 52.7 1.0
OAK A:E58203 4.1 66.2 1.0
CG A:GLU58 4.2 21.4 1.0
CB A:ASP78 4.2 23.2 1.0
CAQ A:E58203 4.3 69.2 1.0
N A:GLY24 4.3 19.7 1.0
CB A:ASP23 4.4 24.0 1.0
CAD A:E58203 4.5 72.6 1.0
NAF A:E58203 4.6 75.1 1.0
CA A:ASP23 4.6 19.7 1.0
C A:ASP78 4.6 25.9 1.0
CAL A:E58203 4.7 76.9 1.0
O A:ASP78 4.8 27.0 1.0
CA A:ASP78 4.8 23.3 1.0
OD1 A:ASP139 4.8 39.7 1.0
N A:SER79 4.9 22.5 1.0
C A:GLY24 4.9 27.0 1.0
N A:ASP78 4.9 22.3 1.0
CAC A:E58203 4.9 75.0 1.0

Manganese binding site 2 out of 2 in 7xis

Go back to Manganese Binding Sites List in 7xis
Manganese binding site 2 out of 2 in the Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:32.9
occ:1.00
 OAJ A:E58203 1.8 40.1 1.0
OD2 A:ASP23 2.0 28.9 1.0
OD1 A:ASP139 2.2 39.7 1.0
CAI A:E58203 2.3 58.0 1.0
OD2 A:ASP78 2.4 25.9 1.0
OAK A:E58203 2.6 66.2 1.0
CG A:ASP23 3.0 26.4 1.0
CG A:ASP139 3.0 36.1 1.0
MN A:MN201 3.2 22.3 1.0
OD1 A:ASP23 3.3 27.0 1.0
CAE A:E58203 3.4 69.8 1.0
CG A:ASP78 3.4 28.1 1.0
CB A:ASP139 3.5 31.3 1.0
CAL A:E58203 3.7 76.9 1.0
OD1 A:ASP78 3.8 24.6 1.0
OAA A:E58203 4.0 75.2 1.0
OD2 A:ASP139 4.1 40.0 1.0
ND2 A:ASN135 4.3 26.9 1.0
CA A:ASP139 4.3 28.0 1.0
CB A:ASP23 4.4 24.0 1.0
CAQ A:E58203 4.4 69.2 1.0
CB A:ALA128 4.4 35.5 1.0
CAD A:E58203 4.4 72.6 1.0
OD1 A:ASN135 4.4 27.2 1.0
OAR A:E58203 4.6 93.5 1.0
CAM A:E58203 4.6 84.2 1.0
CB A:ASP78 4.7 23.2 1.0
CG A:ASN135 4.8 28.1 1.0
O A:ASN135 4.9 28.2 1.0

Reference:

H.Lu, Y.Komukai, K.Usami, Y.Guo, X.Qiao, M.Nukaga, T.Hoshino. Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds For Hiv-1 Rnase H Activity. J.Chem.Inf.Model. 2022.
ISSN: ESSN 1549-960X
PubMed: 36184946
DOI: 10.1021/ACS.JCIM.2C00537
Page generated: Sun Oct 6 11:05:47 2024

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